Plant artificial chromosome platforms via telomere truncation

ABSTRACT

The invention provides engineered plant minichromosomes generated by telomere mediated truncation of native chromosomes. These minichromosomes are faithfully transmitted from one generation to the next and provide an ideal platform for breeding genes into desired plant varieties with out problems, such as linkage drag, associated with standard breeding methods.

This application claims the priority of U.S. Provisional PatentApplication Ser. No. 60/798,830, filed May 9, 2006, and of U.S.Provisional Patent Application Ser. No. 60/862,733, filed Oct. 24, 2006,the entire disclosures of which are specifically incorporated herein byreference.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The invention relates to the fields of molecular biology and plantgenetics. More specifically, the invention relates to plant artificialminichromosome platforms and methods for their production and use.

2. Description of Related Art

Maintenance and inheritance of chromosomes in an organism typicallyrequires three essential elements: origins of replication, a centromereand telomeres, as previously identified with yeast artificialchromosomes. Murray and Szostak (1983) for example described a cloningsystem based on the in vitro construction of linear yeast artificialchromosomes. However, none of the nucleic acid elements that wereidentified are sufficient to maintain artificial chromosomes inmulticellular eukaryotic systems.

One method for generating an artificial chromosome is by de novoconstruction, i.e., assembly of centromeres, telomeres and selectablemarkers and reintroduction into plants (U.S. Pat. No. 7,015,372).However, chromosomes are known to have a minimal size limit forefficient transmission through meiosis (Schubert, 2001). Although mostde novo mammalian minichromosomes can transmit during mitosis, thetransmission of such minichromosomes in germlines has not been reported.The only meiotically transmitted de novo artificial chromosomes ineukaryotes to date are yeast artificial chromosomes (Murray and Szostak,1983; Murray and Szostak, 1986). Additionally, it has been indicatedthat plant centromeres need to be greater than about one megabase insize for normal transmission (Kaszas and Birchler, 1998) and this sizeis larger than can currently be assembled in vitro.

In contrast, some truncated chromosomes with native centromeres aretransmissible through meiosis (Shinohara et al., 2000; Tomizuka et al.,1997, 2000; Voet et al., 2001; Shen et al., 1997, 2000; Schubert, 2001;Zheng et al., 1999; Kato et al., 2005; McClintock, 1938; Brock andPryor, 1996; Nasuda et al., 2005). One method for truncating chromosomesthat has been applied in mammalian systems is telomere mediatedtruncation (Farr et al., 1991, 1992, 1995; Barnett et al., 1993; Itzhakiet al., 1992; Heller et al., 1996; Mills et al., 1999; Saffery et al.,2001). However, no method for telomere mediated truncation of plantchromosomes has been described to date.

Other methods of chromosome deletion have been applied to plant systems.For example, altered maize chromosomes have been generated by X-ray orgamma irradiation of maize pollen (McClintock, 1938; Brock and Pryor,1996) or through a B-9 translocation with duplicated 9S (Zheng et al.,1999; Kato et al., 2005). However, altered chromosomes created by thesemethods have lacked stable transmission during meiosis or mitosis, donot carry site specific recombination sites, have not enabled efficientexpression of heterologous sequences or have been difficult to produce.Thus, there remains a great need in the art for methods of producing andusing plant minichromosomes.

SUMMARY OF THE INVENTION

The invention overcomes limitations in the art by providing plantminichromosomes that can be efficiently transmitted through mitosis andmeiosis. The term “minichromosome” refers to engineered chromosomes madeby deleting portions of a native chromosome. Thus, minichromosomes aredistinct from artificial chromosomes made de novo by recombinant DNAtechniques. In specific embodiments, plant minichromosomes describedherein are provided derived from a starting, native plant chromosomethat is truncated by the insertion of telomere repeats. Thus, plantminichromosomes of the invention may be defined as comprising at leastone chromosome arm that has been truncated. In some further embodiments,a plant minichromosome is truncated in both arms. A plantminichromosomes may, in some aspects, be efficiently transmitted duringmitosis and meiosis in a plant that is the same species as the plant ofthe starting chromosome. It will be understood by one of skill in theart that such minichromosomes generally comprise a functional centromereand origins of replication, both of which allow faithful maintenance.

In one aspect of the invention, a plant minichromosome comprises anative centromere. Native centromeres are found on endogenouschromosomes and are comprised of centromere repeats (Jiang et al.,2003). These sequences provide for efficient segregation of chromosomesduring cell division such as mitosis and meiosis. Thus, in certainaspects of the invention a plant minichromosome is defined as comprisinga native plant centromere sequence. In further embodiments aminichromosome of the invention may be defined as not comprising aneocentromere.

A minichromosome may further comprise engineered telomere sequences. Asused herein the term “engineered telomere sequence” refers to telomeresequence that are in a different context than those found in a nativechromosome. For example, engineered telomere sequences may be in adifferent position relative to the centromere than telomeres found in anative chromosome. In particular, engineered telomere sequences inminichromosomes of the invention may be closer to the centromere of theminichromosome as compared to a native telomere. For example, in a plantminichromosome of the invention, an engineered telomere sequence may bedefined as about 10 kb to about 10 Mb from the centromere of the nativechromosome sequence. In more specific embodiments, an engineeredtelomere may be about 10 kb to about 5 Mb or about 100 kb to about 1, 2,3, 4, or 5 Mb from the centromere of a native chromosome sequences.Plant minichromosomes of the invention may further comprise twoengineered telomere sequences, which may be different distances from thecentromere of the minichromosome.

Engineered telomere sequences may be from a variety of sources. Forexample, engineered telomere sequences may be from the same plantspecies or variety as the native chromosome sequences or from adifferent plant species relative to the native chromosome sequences. Forexample, telomere sequences may be the cloned telomere sequences frompAtT4 comprising direct repeats of the Arabidopsis-type telomeric motif,TTTAGGG (SEQ ID NO:1), or derivatives thereof (Richards and Ausubel,1988). In this case each repeat comprises 430 base pairs of telomericsequence. Engineered telomere repeat sequences may be from maize, wheat,oats, rice, Arabidopsis or soybean. It will be understood by the skilledartisan that engineered telomeres may comprise a plurality of telomererepeat sequences. For example, in certain embodiments an engineeredtelomere of the invention may comprise between 2 and 100, 2 and 50 or 2and 10 repeats, including 6 repeats. In some embodiments of theinvention, telomere sequences in a telomere truncation vector such asthose exemplified herein (e.g., pWY76, pWY86 and pJV21) are provided. Inone embodiment of the invention, a telomere truncation vector may beemployed to generate a truncated minichromosome. The telomere truncationvector may be comprised on the minichromosome or may be separate fromit. In one embodiment of the invention, the telomere truncation vectormay become deleted during the generation of the minichromosome. Atransgene could then, for example, be introduced into the minichromosometo generate a minichromosome comprising one or more added transgene(s).A minichromosome formed by such methods comprises one embodiment of theinvention.

One aspect of plant minichromosomes is their size. Minichromosomesdescribed herein preferably encode a minimal number of endogenous genesthat may deleteriously affect the phenotype of a plant comprising theminichromosome. Thus, it may be preferred that a large portion of anendogenous chromosome be deleted to make a minichromosome, whilemaintaining a sufficient size for stable transmission. This may beimportant when the native chromosome is an A chromosome. B chromosomesdo not typically encode essential functions and therefore may be lesslikely to create deleterious phenotypes. Nonetheless, it has also beenobserved that minichromosomes that are too small are not faithfullymaintained through mitosis and meiosis. Thus, in certain embodiments ofthe invention, a plant minichromosome comprises a native plantchromosome sequence wherein about 1 to about 99.9 percent of the nativechromosome sequence is deleted. In some embodiments, about 10, 20, 25,35, 50, 75, 85, 90, 93, 95, 97, 99, 99.5 or 99.9 percent or any rangederivable therein of the native chromosome sequence is deleted in aminichromosome.

In certain further aspects of the invention, a plant minichromosome maybe defined by its size. For example, a plant minichromosome may bedefined as about 0.1 to about 20 or 30 Mb in size. In furtherembodiments, a plant minichromosome may be about 1, 1.5, 2, 2.5, 3, 4,5, 7.0, 9, 10, 20, 50 or 100 Mb in size or any ranger derivable therein.For instance, in some instances plant minichromosomes described hereinare between about 1 and 10 Mb or between about 5 and 10 Mb in size.

In some aspects of the invention, a plant minichromosome may be definedas being transmitted through mitosis with a 100% frequency. In furthercases, a plant chromosome is defined by the frequency with which it istransmitted during meiosis. For instance, a plant minichromosome may betransmitted with greater than about a 10%, 20%, 25% or 30% frequencyduring meiosis (50% being perfect transmission). Thus, a plantchromosome of the invention may comprise a truncated A or B chromosomethat is transmitted with greater than 35% frequency during meiosis whenthe minichromosome is transmitted in a plant of the same species as thestarting chromosome.

A variety of plants may be used to make plant minichromosomes accordingto the invention. In some embodiments, the plant is defined as a dicotor monocot plant. For example, the plant may be alfalfa, Tripsacum,corn, canola, rice, soybean, tobacco, turfgrass, oat, rye, Arabidopsisor wheat. In certain aspects of the invention, the minichromosome may bedefined as from a maize plant.

In further embodiments, a plant minichromosome of the invention may bederived from a plant A chromosome. For example, the minichromosome maycomprise native chromosome sequences from an A chromosome e.g., in thecase of a maize minichromosome it may comprise native sequences frommaize chromosome 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In one embodiment aplant minichromosome of the invention is derived from a maize chromosome7.

In still further embodiments, a plant minichromosome of the inventioncomprises native chromosome sequences of a plant B chromosome. Forcertain applications telomere truncated B chromosomes may providebenefit as they comprise non-essential genes that are not expected tointerfere with plant phenotype or with expression of transgenes from thechromosome. The telomere truncation methods described herein result indeletion of native chromosomal sequences from the B chromosome,particularly those regions that are distal from the centromere. Bydeletion of regions of the B chromosome that control non-disjunctionthrough telomere truncation, minichromosomes based on B chromosomes willsegregate normally. Virtually any type of plant B chromosomes may beused as described herein to make a plant minichromosomes. For example, aplant minichromosome may comprise native B chromosome sequences frommaize, rye or sorghum or from any other plant species with B chromosomesor any species comprising a B chromosome that has been introduced (Jonesand Rees, 1982). In some embodiments, chromosomal truncation may becarried out in a plant cell comprising multiple B chromosomes, such as acell comprising at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or more Bchromosomes copies.

In certain aspects of the invention, it may be preferred that aminichromosome comprising plant lacks B chromosomes as presence of anintact B chromosome may cause non-disjunction of B chromosome derivedminichromosomes. Thus, in some embodiments, the invention provides amethod for manipulating the dosage of a plant minichromosome comprisingB chromosomes sequences by introduction of an intact B chromosome or aportion of a B chromosome. For example, the dosage of a plantminichromosome may be modulated by introducing B chromosome sequencethat controls B centromere nondisjunction.

A plant minichromosome according to the invention may comprise aselectable marker which confers a growth advantage under particularconditions to plant cells carrying the marker, thereby allowingidentification of plants, plants cells or plant parts comprising theminichromosome. A selectable marker may function in bacterial cells. Aminichromosome may also comprise “negative” selectable markers whichconfer susceptibility to an antibiotic, herbicide or other agent,thereby allowing for selection against plants, plant cells or cells ofany other organism of interest comprising the particular minichromosome.Furthermore, in some aspects, a plant minichromosome may comprise a malefertility restoration gene such as a Rf3 gene.

A plant minichromosome may further comprise site-specific recombinationsequences. For example, minichromosomes of the invention may comprise alox or FRT site. Site-specific recombination provides a convenientmethod for moving genes in and out of artificial chromosomes such as theplant minichromosomes of the invention. Random mutagenesis can also beprovided in this manner. Methods for using site-specific recombinationto mediate in vivo gene transfer are well known in the art.Site-specific recombination may be used to sequentially add genes to aminichromosome in order to provide the genes for an entire biochemicalpathway or a set of agronomically elite characteristics. In some aspectsof the invention telomere sequence inserted into a starting plantchromosome comprise a site specific recombination sequences. In thisaspect plant minichromosomes comprising site specific recombinationsequences may be rapidly generated.

In certain further embodiments, a plant minichromosome may comprisegenes which control the copy number of the minichromosome within a cell.One example of such a gene is the element of B chromosomes that mediatesnon-disjunction as described above. One or more structural genes mayalso be comprised within a minichromosome. Specifically contemplated asbeing useful are as many structural genes as may be inserted into aminichromosome while still maintaining a functional and faithfullytransmitted artificial chromosome. This may include one, two, three,four, five, six, seven, eight, nine or more structural genes.

In another embodiment, the invention provides methods for expressing oneor more foreign genes in plants, plant cells or cells of any otherorganism of interest. The foreign gene(s) may be from any organism,including plants, animals and bacteria. In one embodiment, foreigngene(s) confer improved agronomic characteristics to a given plant. Forexample, the transgene may confer a trait such as insect resistance,herbicide tolerance, altered carbohydrate metabolism, altered fatty acidmetabolism, disease resistance, and pest resistance. It is furthercontemplated that minichromosomes may be used to simultaneously transfermultiple foreign genes to a plant comprising entire biochemical orregulatory pathways. In yet another embodiment, it is contemplated thatthe plant minichromosomes can be used as DNA cloning vectors. Such avector could be used in plant and animal sequencing projects. In somespecific cases, a transgene may be introduced into a starting chromosomealong with telomere repeat sequences thereby generating a plantminichromosome comprising the transgene.

In a further embodiment there is provided a plant cell comprising the aplant minichromosome. The plant cell may be the same species as thespecies of the starting plant chromosome, however in certain cases itmay be a different species. Thus, a plant or a plant seed comprising aplant minichromosome also forms part of the invention. In certainaspects a plant comprising the minichromosome is a maize plant.

In general methods and compositions of the invention involve telomeremediated chromosome truncation. For example, a vector comprising planttelomeres is introduced into a plant cell. Such vectors may beintroduced into a plant cell by any of the methods that are well knownin the art, for example DNA bombardment or Agrobacterium mediatedtransformation. For example, in certain embodiments, Agrobacteriummediated transformation may be used to generate plant minichromosomesderived from A chromosomes. Conversely, in some case DNA bombardment maybe used to generate plant minichromosomes derived from B chromosomes.Upon integration of the telomere sequences into one or more positions ofa plant chromosome the chromosome will be truncated at the point ofintegration. Thus, a method of the invention may comprise transforming astarting plant chromosome with a heterologous nucleic acid comprising atleast two telomere repeat sequences and allowing truncation of thestarting plant chromosome to occur to produce a plant minichromosome.One or both arms of a chromosome may be truncated by telomereintegration. Resultant plant minichromosomes may then be screened todetermine their size and origin, for example by Southern blot or FISH.

In some further methods of the invention, a starting plant chromosome istransformed with heterologous nucleic acid sequence comprising telomererepeats and additional sequences such as site specific recombinationsequences a transgene or other selected sequence. Alternatively, astarting plant chromosome may be transformed with heterologous nucleicacid sequence comprising telomere repeats to generate a plantminichromosome. Subsequently, the plant minichromosome may betransformed with a second heterologous nucleic acid sequence comprisingan additional sequence such as a transgene. For example, additionalsequences may comprise an FRT or lox site. In some cases, additionalsequence may also comprise a gene that confers insect resistance,herbicide tolerance, altered carbohydrate metabolism, altered fatty acidmetabolism, disease resistance, male fertility restoration or pestresistance. Thus, in certain embodiments, the additional gene may be amale fertility restoration gene such as an Rf3 gene. This aspect of theinvention may be particularly advantageous since plant minichromosomesthat restore male fertility may be transmitted to progeny cells withvery high efficiency.

Embodiments discussed in the context of a methods and/or composition ofthe invention may be employed with respect to any other method orcomposition described herein. Thus, an embodiment pertaining to onemethod or composition may be applied to other methods and compositionsof the invention as well.

As used herein the specification, “a” or “an” may mean one or more. Asused herein in the claim(s), when used in conjunction with the word“comprising”, the words “a” or “an” may mean one or more than one.

The use of the term “or” in the claims is used to mean “and/or” unlessexplicitly indicated to refer to alternatives only or the alternativesare mutually exclusive, although the disclosure supports a definitionthat refers to only alternatives and “and/or.” As used herein “another”may mean at least a second or more.

Throughout this application, the term “about” is used to indicate that avalue includes the inherent variation of error for the device, themethod being employed to determine the value, or the variation thatexists among the study subjects.

Other objects, features and advantages of the present invention willbecome apparent from the following detailed description. It should beunderstood, however, that the detailed description and the specificexamples, while indicating preferred embodiments of the invention, aregiven by way of illustration only, since various changes andmodifications within the spirit and scope of the invention will becomeapparent to those skilled in the art from this detailed description.

BRIEF DESCRIPTION OF THE FIGURES

The following drawings form part of the present specification and areincluded to further demonstrate certain aspects of the presentinvention. The invention may be better understood by reference to one ormore of these drawings in combination with the detailed description ofspecific embodiments presented herein.

FIG. 1: Examples of chromosomal truncation constructs. Constructs pWY76and pWY86, and the control construct pWY96 are diagrammed. The meaningof the letter designations in the figure are as follows: LB, T-DNA leftborder; RB, T-DNA right border; Tvsp, terminator from soybean vegetativestorage protein gene; Bar, bialaphos resistance gene as a selectablemarker gene; TEV, tobacco etch virus 5′ untranslated region; P35S, 2X35Spromoter from cauliflower mosaic virus (CaMV); Tnos, Nos terminator fromAgrobacterium tumefaciens; Tmas, Mas terminator from A. tumefaciens;Pnos, Nos promoter from A. tumefaciens; Pmas1′, Mas promoter from A.tumefaciens; lox and FRT, site-specific recombination sites; HPT,hygromycin B resistance gene; GFP, green fluorescent protein gene;DsRed, red fluorescent protein; FLP, site specific recombinase gene;Telomeres, telomere units of pAtT4 isolated from Arabidopsis thaliana(Richards and Ausubel 1988). The arrows indicate the direction oftranscription or in the case of the telomere repeats, the chromosomalorientation.

FIG. 2: Structure of pJV21. The four functional parts are indicated bybrackets and labeled. LB, left border; RB, right border; lox, lox66site; Cre, Cre recombinase gene; bar, bialaphos resistance gene; 35S,CaMV 35S promoter; ubi, maize ubiquitin promoter; n3′, terminatorsequence of the nopaline synthase gene; telo, 400 bp telomere repeatsfrom Arabidopsis; NotI and AscI, restriction enzyme sites.

DETAILED DESCRIPTION OF THE INVENTION

One of the goals of plant breeding is the selection of desirablecharacteristics such as disease and insect resistance, rate of growth,nutrient requirements and yield. Unfortunately, in many plant speciesdifferent varieties are optimal for geographic and climactic regions.However, breeding a desirable characteristic or gene into each varietycan take years since any given characteristic must be selected for whilemaintaining the specific advantages of a given variety. Modifying sometraits or stacking of traits can also require multiple transgenes, whichcomplicates introgression. Thus, ideally genes that impart agronomicallysuperior characteristics could be provided on a separate chromosome andthus would be unlinked to other genes and easily selected in progenyplants. However, until now a plant minichromosome that is capable ofencoding genes had not been described.

The invention overcomes limitations in the art by providing plantminichromosomes that may be used to incorporate desirable transgenes. Incertain cases, the minichromosome can be introgressed into anyparticular variety of plant since it will not be linked to anybackground genes, encoded on other chromosomes. These minichromosomesmay further comprise site specific recombination sites that enable genesto be quickly moved in or out of any plant variety comprising theminichromosome. Thus, these new plant minichromosomes reduce theproblems associated with linkage drag by providing a geneticallyisolated expression platform.

I. Recombination Systems

In certain embodiments of the invention plant minichromosomes compriseat least one site specific recombinase site. Site-specific integraserecombinase systems have been identified in several organisms including,but not limited to, the Cre/lox system of bacteriophage P1 (Abremski etal., 1983; U.S. Pat. Nos. 4,959,317; 5,658,772), the FLP/FRT system ofyeast (Golic and Lindquist, 1989), the Pin recombinase of E. coli(Enomoto et al., 1983), the Gin/gix recombinase of phage Mu (Maeser etal., 1991), the R/RS system of the pSR1 plasmid from Zygosaccharomycesrouxii (Onouchi et al., 1991; Araki et al., 1992) and the R recombinasefrom Zygosaccharomyces rouxii (Onouchi et al., 1995). All of thesesystems have been shown to function in plants (O'Gorman et al., 1991;Maeser et al., 1991; Onouchi et al., 1991; Dale and Ow, 1991). It isbelieved that site-directed integration systems like Cre/lox or FLP/FRTrequire a circular DNA intermediate. Of these systems, Cre/lox andFLP/FRT have been widely utilized.

The FLP/FRT system is native to the yeast Saccharomyces cerevisiae(Golic and Lindquist, 1989; reviewed in Futcher, 1988). In yeast, therecombinase enzyme (FLP) resides on a 2μ plasmid and recognizes 599 basepair (bp) inverted repeats (FRT) as target sites. The minimal functionalsequence unit within the 599 bp repeats includes only 34 bp; two 13 bpinverted repeats separated by an asymmetric 8 bp spacer region althougha third, non-essential repeat of the 13 bp sequence is often present(Sauer, 1994). FLP-mediated rearrangement of DNA flanked by invertedrepeats of FRT sequence often results in the inversion of the DNAbetween the FRT target sites. In this case, both FRT sites are retained.FLP recombinase can also recognize directly repeated FRT target sites.FLP-mediated rearrangements of DNA flanked by directly repeated FRTsites often results in the excision of the DNA located between the FRTtarget sites. In this case, the excised DNA is released in circular formcomprising one FRT site while the second FRT site remains on thetemplate DNA molecule. FLP recombinase can also mediate recombinationbetween FRT sites on different DNA molecules; for example, FLPrecombinase can mediate recombination between FRT sites on differentchromosomes. Sadowski (1995) has shown that recombination catalyzed byFLP/FRT is reversible in nature.

The DNA exchange catalyzed by FLP/FRT can be carried out in vitro aspurified FLP recombinase has been shown to mediate recombination betweenFRT sites (Meyer-Leon et al., 1984). The yeast FLP/FRT combination hasalso been used to direct site-specific recombination, both excision andamplification of sequences flanked by FRT sites, in Escherichia coli(Cox, 1983) as well as in Drosophila genomes (Golic and Lindquist, 1989;Golic, 1994). FLP/FRT has also been employed to direct site-specificexcision of parts of transgenes from plasmid DNA in maize and riceprotoplasts by homologous recombination (see, for example, U.S. Pat. No.5,527,695). FLP/FRT has also been utilized in stably transformed maizefor site-directed excision of sequences inserted into the maize genomewhich are flanked by FRT sites (U.S. Pat. Nos. 5,929,301 and 6,175,058).Site-specific chromosomal targeting of foreign DNA into bacterial andmammalian chromosomes can also be effected by FLP/FRT (Huang et al.,1991; O'Gorman et al., 1991) and this insertion by FLP into FRT siteshas been shown to be reversible in non-yeast genomes (Huang et al.,1997). It is possible to sufficiently alter FRT sites such thatrecombination occurs but is not reversible (U.S. Pat. No. 6,187,994) orfavors a forward reaction relative to a reverse reaction (Senecoff etal., 1988).

A second well characterized recombination system is that of Cre/lox frombacteriophage P1 (Abremski et al., 1983; reviewed in Craig, 1988; Sauer,1994; Ow, 1996). Cre recombinase (causing recombination) recognizes lox(locus of crossing over (x)) target sequences and mediates site-specificrecombination between compatible lox sites. Compatible sites may or maynot comprise identical sequences. Lox sites are 34 base pairs in length,comprising two 13 bp inverted repeats separated by 8 bp of other spacernucleotides. Lox sequences include loxP from bacteriophage P1 (Albert etal., 1995) as well as loxB, loxL, and loxR sites which are nucleotidesequences isolated from E. coli (Hoess et al., 1982). Functionalvariants of loxP sites reported include, but are not limited to lox66,lox71, and lox72 (Albert et al., 1995; Langer et al., 2002). Loxsequences can also be produced by a variety of synthetic techniqueswhich are known in the art. Examples of synthetic techniques forproducing functional lox sites are disclosed by Ogilvie et al. (1981)and Ito et al. (1982).

The lox site is an asymmetrical nucleotide sequence and as such, loxsites on the same DNA molecule can have the same or opposite orientationwith respect to each other. Recombination between lox sites in the sameorientation results in a deletion of the DNA segment located between thetwo lox sites. In this case, ligation between the resulting ends of theoriginal DNA molecule occurs and a lox site is retained. The deleted DNAsegment forms a circular molecule of DNA which also contains a singlelox site. Recombination between lox sites in opposite orientations onthe same DNA molecule results in an inversion of the nucleotide sequenceof the DNA segment located between the two lox sites. In addition,reciprocal exchange of DNA segments proximate to lox sites located ontwo different DNA molecules can occur. All of these recombination eventsare catalyzed by the product of the Cre coding region and arereversible. It is possible, however, to sufficiently alter lox sitessuch that recombination events occur but are resistant to the reverserecombination reaction (Albert et al., 1995; Araki et al., 1997; PCTPublication WO 01/11058) or such that two sites are “non-compatible”recombination substrates for the recombinase (Hoess et al., 1986; Trinhand Morrison, 2000; Lee and Saito, 1988; EP 1 035 208). It is alsopossible to prevent the reverse reaction from occurring be removing thesource of recombinase, for example, by breeding or use of particularregulatory promoters.

Cre recombinase also effects site-directed integration. For example, alacZ reporter gene was integrated into the genome of Chinese HamsterOvary (CHO) cells using Cre-recombinase, a single lox site on the lacZtargeting vector and a single lox site previously located within the CHOgenomic DNA (Fukushige and Sauer, 1992). Cre recombinase has been shownto mediate recombination between lox sites in yeast (Sauer, 1987) andplants, such as tobacco and Arabidopsis (see, for example, U.S. Pat. No.5,658,772; Medberry, et al., 1995; Albert et al., 1995) as well as inmammalian cells such as mice (Sauer and Henderson, 1988; Fukushige andSauer, 1992; Sauer, 1998). Site-specific integration of large BAC(bacterial minichromosome) fragments into plant and fungal genomesutilizing a Cre/lox recombination system has also been reported (Choi etal., 2000). It is believed that in order to achieve site-directedintegration into a single genomic lox site, a circular DNA moleculecomprising a single lox site must be introduced into the cell.Therefore, the methods of the present invention make it possible toachieve site-directed integration of DNA molecules lacking ancillarysequences that are often present in order to replicate and maintain thecircular molecules in a bacterial host cell. Wallace et al., (2000) andDay et al., (2000) discuss the use of site-directed integration as amethod to pre-select sites in the genome for repeatable expression oftransgenes in embryonic stem cells or tobacco, respectively.

Cre recombinase can contact and effect recombination utilizing a numberof lox sites including, but not limited to loxP and a number of variantsof the wild type loxP site such as lox66 (Albert et al., 1995). The DNAexchange directed by the lox sites occurs in the 8 bp spacer region andessentially effects an exchange of the 13 bp inverted repeats of the twolox sites involved. For example, site-directed recombination in which asingle lox site on one DNA molecule recombines with a second single loxsite on a second DNA molecule generates a sequence in which theintegrated DNA is flanked by a lox site on either side. When the singlelox sites on the separate molecules involved are identical, the tworesultant lox sites adjacent to the inserted DNA are also identical. If,however, the two single lox sites on the starting molecules arenon-identical in the 13 bp inverted repeats, the two resultant lox sitesadjacent to the inserted DNA will differ from the starting lox sites.For example, if a first single lox66 site is involved in site-directedintegration with a second single lox71 site, the resultant lox sitesflanking the inserted DNA comprise sequences of loxP and lox72 sites(Albert et al., 1995).

Site-directed integration utilizing identical lox or FRT sites on thetwo recombining molecules results in the inserted DNA being flanked byidentical recombination sites, a reaction that is easily reversed by therecombinase. To prevent the deletion of the inserted sequence, it isoften desirable to remove the source of recombinase enzyme, for example,by segregation or by placing the recombinase gene under the control ofan inducible promoter and removing the inducing source. Alternatively,one of skill in the art may use site-specific recombination sequencesdesigned such that after the integration reaction, the resultant sitesare non-compatible for a reverse reaction or recombine at a reducedrate.

One of skill in the art will recognize that the integrase enzyme, suchas Cre or FLP recombinase, can be provided to the target site or sites,such as lox or FRT, by any means known in the art. For example, therecombinase can be transiently supplied by expression from a gene, andappropriate control sequences, that reside on a separately maintainedplasmid within the host cells. The recombinase gene and appropriatecontrol sequences can be inserted into the genome of the organism andstably expressed in the host cells. Alternatively, sexual crossing orbreeding may be used to introduce the recombinase to cells containingthe target lox or FRT site or sites; in this instance, an organism suchas plant containing the recombinase gene could be crossed to a plantcontaining the target lox or FRT sites and progeny from this union wouldcontain both the recombinase and the target site or sites. In somecases, mRNA coding for the desired recombinase can be introduced intothe host cells to encode and provide the recombinase protein. In othercases, one may introduce isolated recombinase protein into a host cellcomprising a target recombination site. In any of these cases, thepromoter directing recombinase expression may be, but not limited to,constitutive or inducible in manner. One of skill in the art will alsorecognize that the genes for recombinase genes such as Cre or FLP may beisolated from bacteriophage P1 or Saccharomyces cerevisiae,respectively, and utilized directly in a new host system or the genesequence may be optimized for codon usage for expression in thetransgenic host. In a similar fashion, one of skill in the art willrecognize that natively occurring as well as synthetic target sites maybe recognized and mediate recombination with an appropriate recombinase.

Examples of recombinase mediated gene replacement or gene excisiontypically utilize two target sites flanking the sequence to be replacedor excised. For example, Odell et al. (U.S. Pat. No. 5,658,772) disclosethe use of two loxP sites and Cre-recombinase to generate specific genereplacements in tobacco. The Cre/lox system has also been used in aninducible manner to activate and to remove transgenes in transgenicplants (PCT Publication WO 01/40492). Baszczynski et al. (U.S. Pat. No.6,187,994) disclose the use of multiple, non-identical FRT sites andFLP-recombinase to generate a variety of gene alterations in maize.Baszczynski et al. (U.S. Pat. No. 6,262,341) also disclose the use of achimeric Cre/FLP recombinase with dual target site specificity to effectrecombination of DNA sequences flanked by a lox sequence on one side anda FRT sequence on another side. In each of these cases, the integrationor excision of sequences generates extraneous DNA fragments as part ofthe recombination schema. Site-directed integration, however, mayutilize only one target site in the recipient genome. The presentinvention proposes Cre-mediated, targeted integration of anon-replicating, in vitro generated, transformation-ready circularmolecule containing a first single lox site into a second single loxsite previously introduced into the target genome.

II. Genes for Use in the Invention

It will be understood by one of skill in the art that minichromosomes ofthe instant invention may be used to express a variety of genes. In somepreferred embodiments such genes confer agronomically elitecharacteristics to a plant comprising a minichromosome of the invention.Some none limiting examples of genes for use in the instant inventionare provided below.

A. Herbicide Resistance

Numerous herbicide resistance genes are known and may be employed withthe invention. An example is a gene conferring resistance to a herbicidethat inhibits the growing point or meristem, such as an imidazalinone ora sulfonylurea. Exemplary genes in this category code for mutant ALS andAHAS enzyme as described, for example, by Lee et al., (1988); Gleen etal., (1992); and Miki et al., (1990).

Resistance genes for glyphosate (resistance conferred by mutant5-enolpyruvl-3 phosphoshikimate synthase (EPSP) and aroA genes,respectively) and other phosphono compounds such as glufosinate(phosphinothricin acetyl transferase (PAT) and Streptomyceshygroscopicus phosphinothricin-acetyl transferase (bar) genes) may alsobe used. See, for example, U.S. Pat. No. 4,940,835 to Shah, et al.,which discloses the nucleotide sequence of a form of EPSPS which canconfer glyphosate resistance. A DNA molecule encoding a mutant aroA genecan be obtained under ATCC accession number 39256, and the nucleotidesequence of the mutant gene is disclosed in U.S. Pat. No. 4,769,061 toComai. European patent application No. 0 333 033 to Kumada et al., andU.S. Pat. No. 4,975,374 to Goodman et al., disclose nucleotide sequencesof glutamine synthetase genes which confer resistance to herbicides suchas L-phosphinothricin. The nucleotide sequence of aphosphinothricin-acetyltransferase gene is provided in Europeanapplication No. 0 242 246 to Leemans et al. DeGreef et al., (1989),describe the production of transgenic plants that express chimeric bargenes coding for phosphinothricin acetyl transferase activity. Exemplaryof genes conferring resistance to phenoxy propionic acids andcyclohexanediones, such as sethoxydim and haloxyfop are the Acct-S1,Accl-S2 and Acct-S3 genes described by Marshall et al., (1992).

Genes are also known conferring resistance to a herbicide that inhibitsphotosynthesis, such as a triazine (psbA and gs+ genes) and abenzonitrile (nitrilase gene). Przibilla et al., (1991), describe thetransformation of Chlamydomonas with plasmids encoding mutant psbAgenes. Nucleotide sequences for nitrilase genes are disclosed in U.S.Pat. No. 4,810,648 to Stalker, and DNA molecules containing these genesare available under ATCC Accession Nos. 53435, 67441, and 67442. Cloningand expression of DNA coding for a glutathione S-transferase isdescribed by Hayes et al., (1992).

B. Male Sterility and Restoration of Male Fertility

Examples of genes conferring male sterility as well as restorers of malefertility are known in the art and include those disclosed in U.S. Pat.Nos. 3,861,709, 3,710,511, 4,654,465 , 4,727,219, 5,530,191, 5,625,132,and 5,689,041, each of the disclosures of which are specificallyincorporated herein by reference in their entirety.

Male sterility genes can increase the efficiency with which hybrids aremade, in that they eliminate the need to physically emasculate the cornplant used as a female in a given cross.

Where one desires to employ male-sterility systems with a corn plant inaccordance with the invention, it may be beneficial to also utilize oneor more male-fertility restorer genes. For example, where cytoplasmicmale sterility (CMS) is used, hybrid seed production requires threeinbred lines: (1) a cytoplasmically male-sterile line having a CMScytoplasm; (2) a fertile inbred with normal cytoplasm, which is isogenicwith the CMS line for nuclear genes (“maintainer line”); and (3) adistinct, fertile inbred with normal cytoplasm, carrying a fertilityrestoring gene (“restorer” line). The CMS line is propagated bypollination with the maintainer line, with all of the progeny being malesterile, as the CMS cytoplasm is derived from the female parent. Thesemale sterile plants can then be efficiently employed as the femaleparent in hybrid crosses with the restorer line, without the need forphysical emasculation of the male reproductive parts of the femaleparent.

The presence of a male-fertility restorer gene results in the productionof fully fertile F₁ hybrid progeny. If no restorer gene is present inthe male parent, male-sterile hybrids are obtained. Such hybrids areuseful where the vegetative tissue of the corn plant is utilized, e.g.,for silage, but in most cases, the seeds will be deemed the mostvaluable portion of the crop, so fertility of the hybrids in these cropsmust be restored. Therefore, one aspect of the current inventionconcerns the hybrid corn plant CH389090 comprising a genetic locuscapable of restoring male fertility in an otherwise male-sterile plant.Examples of male-sterility genes and corresponding restorers which couldbe employed with the plants of the invention are well known to those ofskill in the art of plant breeding and are disclosed in, for instance,U.S. Pat. Nos. 5,530,191; 5,689,041; 5,741,684; and 5,684,242, thedisclosures of which are each specifically incorporated herein byreference in their entirety. For example, restorer gene may be an Rf3gene (Duvick, 1965; Chase and Gabay-Laughnan 2004; Gabay-Laughnan etal., 2004) or genes used in the Barnase/Barstar restoration system(Mariani et al., 1990; Mariani et al., 1992)

C. Disease Resistance

Plant defenses are often activated by specific interaction between theproduct of a disease resistance gene (R) in the plant and the product ofa corresponding avirulence (Avr) gene in the pathogen. A plant line canbe transformed with cloned resistance gene to engineer plants that areresistant to specific pathogen strains. See, for example Jones et al.,(1994) (cloning of the tomato Cf-9 gene for resistance to Cladosporiumfulvum); Martin et al., (1993) (tomato Pto gene for resistance toPseudomonas syringae pv.); and Mindrinos et al., (1994) (ArabidopsisRSP2 gene for resistance to Pseudomonas syringae).

A viral-invasive protein or a complex toxin derived therefrom may alsobe used for viral disease resistance. For example, the accumulation ofviral coat proteins in transformed plant cells imparts resistance toviral infection and/or disease development effected by the virus fromwhich the coat protein gene is derived, as well as by related viruses.See Beachy et al., (1990). Coat protein-mediated resistance has beenconferred upon transformed plants against alfalfa mosaic virus, cucumbermosaic virus, tobacco streak virus, potato virus X, potato virus Y,tobacco etch virus, tobacco rattle virus and tobacco mosaic virus.

A virus-specific antibody may also be used. See, for example,Tavladoraki et al., (1993), who show that transgenic plants expressingrecombinant antibody genes are protected from virus attack.

Logemann et al., (1992), for example, disclose transgenic plantsexpressing a barley ribosome-inactivating gene have an increasedresistance to fungal disease.

D. Waxy Starch

The waxy characteristic is an example of a recessive trait. In thisexample, the progeny resulting from the first backcross generation (BC1)must be grown and selfed. A test is then run on the selfed seed from theBC1 plant to determine which BC1 plants carried the recessive gene forthe waxy trait. In other recessive traits additional progeny testing,for example growing additional generations such as the BC1S1, may berequired to determine which plants carry the recessive gene.

E. Insect Resistance

One example of an insect resistance gene includes a Bacillusthuringiensis protein, a derivative thereof or a synthetic polypeptidemodeled thereon. See, for example, Geiser et al., (1986), who disclosethe cloning and nucleotide sequence of a Bt δ-endotoxin gene. Moreover,DNA molecules encoding δ-endotoxin genes can be purchased from theAmerican Type Culture Collection, Manassas, Va., for example, under ATCCAccession Nos. 40098, 67136, 31995 and 31998. Another example is alectin. See, for example, Van Damme et al., (1994), who disclose thenucleotide sequences of several Clivia miniata mannose-binding lectingenes. A vitamin-binding protein may also be used, such as avidin. SeePCT application US93/06487, the contents of which are herebyincorporated by reference. This application teaches the use of avidinand avidin homologues as larvicides against insect pests.

Yet another insect resistance gene is an enzyme inhibitor, for example,a protease or proteinase inhibitor or an amylase inhibitor. See, forexample, Abe et al., (1987) (nucleotide sequence of rice cysteineproteinase inhibitor), Huub et al., (1993) (nucleotide sequence of cDNAencoding tobacco proteinase inhibitor I), and Sumitani et al., (1993)(nucleotide sequence of Streptomyces nitrosporeus α-amylase inhibitor).An insect-specific hormone or pheromone may also be used. See, forexample, the disclosure by Hammock et al., (1990), of baculovirusexpression of cloned juvenile hormone esterase, an inactivator ofjuvenile hormone.

Still other examples include an insect-specific antibody or animmunotoxin derived therefrom and a developmental-arrestive protein. SeeTaylor et al., (1994), who described enzymatic inactivation intransgenic tobacco via production of single-chain antibody fragments.

F. Modified Fatty Acid, Phytate and Carbohydrate Metabolism

Genes may be used conferring modified fatty acid metabolism. Forexample, stearyl-ACP desaturase genes may be used. See Knutzon et al.,(1992). Various fatty acid desaturases have also been described, such asa Saccharomyces cerevisiae OLE1 gene encoding Δ9 fatty acid desaturase,an enzyme which forms the monounsaturated palmitoleic (16:1) and oleic(18:1) fatty acids from palmitoyl (16:0) or stearoyl (18:0) CoA(McDonough et al., 1992); a gene encoding a stearoyl-acyl carrierprotein delta-9 desaturase from castor (Fox et al. 1993); Δ6- andΔ12-desaturases from the cyanobacteria Synechocystis responsible for theconversion of linoleic acid (18:2) to gamma-linolenic acid (18:3 gamma)(Reddy et al. 1993); a gene from Arabidopsis thaliana that encodes anomega-3 desaturase (Arondel et al. 1992)); plant Δ9-desaturases (PCTApplication Publ. No. WO 91/13972) and soybean and Brassica Δ15desaturases (European Patent Application Publ. No. EP 0616644).

Phytate metabolism may also be modified by introduction of aphytase-encoding gene to enhance breakdown of phytate, adding more freephosphate to the transformed plant. For example, see Van Hartingsveldtet al., (1993), for a disclosure of the nucleotide sequence of anAspergillus niger phytase gene. In corn, this, for example, could beaccomplished by cloning and then reintroducing DNA associated with thesingle allele which is responsible for corn mutants characterized by lowlevels of phytic acid. See Raboy et al., (1990).

A number of genes are known that may be used to alter carbohydratemetabolism. For example, plants may be transformed with a gene codingfor an enzyme that alters the branching pattern of starch. See Shirozaet al., (1988) (nucleotide sequence of Streptococcus mutansfructosyltransferase gene), Steinmetz et al., (1985) (nucleotidesequence of Bacillus subtilis levansucrase gene), Pen et al., (1992)(production of transgenic plants that express Bacillus licheniformisα-amylase), Elliot et al., (1993) (nucleotide sequences of tomatoinvertase genes), Sergaard et al., (1993) (site-directed mutagenesis ofbarley α-amylase gene), and Fisher et al., (1993) (maize endospermstarch branching enzyme II). The Z10 gene encoding a 10 kD zein storageprotein from maize may also be used to alter the quantities of 10 kDZein in the cells relative to other components (Kirihara et al., 1988).

III. Plants and Use Thereof

The present invention provides a transgenic plant comprising a plantminichromosome of the invention including, without limitation, alfalfa,corn, canola, rice, soybean, tobacco, turfgrass, oat, rye, and wheat,among others. Also included is a seed from a plant, the seed comprisinga minichromosome of the invention.

For example, in certain embodiments, a seed comprising a minichromosomeof the invention may express a gene that provides for herbicidetolerance. One beneficial example of a herbicide tolerance gene providesresistance to glyphosate, N-phosphonomethyl)glycine, including theisopropylamine salt form of such herbicide.

The present invention can be, in practice, combined with other diseasecontrol traits in a plant to achieve desired traits for enhanced controlof plant disease. Combining disease control traits that employ distinctmodes-of-action can provide protected transgenic plants with superiorconsistency and durability over plants harboring a single control traitbecause of the reduced probability that resistance will develop in thefield.

The invention also relates to commodity products containing one or moreof the minichromosomes of the present invention, and produced from arecombinant plant or seed containing one or more minichromosome. Acommodity product containing one or more of the sequences of the presentinvention is intended to include, but not be limited to, meals, oils,crushed or whole grains or seeds of a plant, or any food productcomprising any meal, oil, or crushed or whole grain of a recombinantplant or seed containing one or more of the sequences of the presentinvention. The detection of one or more of the sequences of the presentinvention in one or more commodity or commodity products contemplatedherein is de facto evidence that the commodity or commodity productcomprises a minichromosome of the invention.

A further aspect of the invention relates to tissue cultures of plantscomprising mini-chromosomes. As used herein, the term “tissue culture”indicates a composition comprising isolated cells of the same or adifferent type or a collection of such cells organized into parts of aplant. Exemplary types of tissue cultures are protoplasts, calli andplant cells that are intact in plants or parts of plants, such asembryos, pollen, flowers, kernels, ears, cobs, leaves, husks, stalks,roots, root tips, anthers, silk, and the like. In a preferredembodiment, the tissue culture comprises embryos, protoplasts,meristematic cells, pollen, leaves or anthers derived from immaturetissues of these plant parts. Means for preparing and maintaining planttissue cultures are well known in the art (U.S. Pat. Nos. 5,538,880; and5,550,318, each incorporated herein by reference in their entirety). Byway of example, a tissue culture comprising organs such as tassels oranthers has been used to produce regenerated plants (U.S. Pat. Nos.5,445,961 and 5,322,789; the disclosures of which are incorporatedherein by reference).

One type of tissue culture in maize is tassel/anther culture. Tasselscontain anthers which in turn enclose microspores. Microspores developinto pollen. For anther/microspore culture, if tassels are the plantcomposition, they are preferably selected at a stage when themicrospores are uninucleate, that is, include only one, rather than 2 or3 nuclei. Methods to determine the correct stage are well known to thoseskilled in the art and include mitramycin fluorescent staining, trypanblue (preferred) and acetocarmine squashing. The mid-uninucleatemicrospore stage has been found to be the developmental stage mostresponsive to the subsequent methods disclosed to ultimately produceplants.

Although microspore-containing plant organs such as tassels cangenerally be pretreated at any cold temperature below about 25° C., arange of 4 to 25° C. is preferred, and a range of 8 to 14° C. isparticularly preferred. Although other temperatures yield embryoids andregenerated plants, cold temperatures produce optimum response ratescompared to pretreatment at temperatures outside the preferred range.Response rate is measured as either the number of embryoids or thenumber of regenerated plants per number of microspores initiated inculture. Exemplary methods of microspore culture are disclosed in, forexample, U.S. Pat. Nos. 5,322,789 and 5,445,961, the disclosures ofwhich are specifically incorporated herein by reference.

Furthermore, in certain embodiments of the invention, a starting plantor plant cell is transformed with a nucleic acid such as a telomeretruncation vector. Methods for transforming plant cells with nucleicacids are well known to those of skill in the art. For example, methodsmay employ Agrobacterium mediated transformation or DNA particlebombardment as exemplified herein. Certain specialized methods fortransforming high molecular weight nucleic acids have also beendeveloped. For instance, the BIBAC system designed by Hamilton andcolleagues (Hamilton, 1997; Hamilton et al., 1996; U.S. Pat. No.5,733,744) for the transformation of large T-DNA inserts to plantgenomes. The BIBAC is a combination of the T-DNA transfer function ofthe Ti plasmid and the capacity of maintaining large DNA fragments ofthe bacterial artificial chromosome (BAC). As with a BAC, it has asingle copy origin of replication from the E. coli F-plasmid for stablemaintenance of the plasmid in E. coli. It also has a single copy originof replication from the Agrobacterium Ri plasmid, and the T-DNA bordersfor T-DNA transformation. A similar system, transformation competentartificial chromosomes (TAC), with an E. coli bacteriophage P1 origin,has also been used in the transformation of large DNAs (Liu et al.,1999).

IV. Breeding of Plants Comprising a Minichromosome

As discussed above a starting, native plant chromosome may be used inaccordance with the invention to generate a plant minichromosome. Insome embodiments, native chromosomes for use in the current inventionwill be maize chromosomes such as maize B chromosomes or a maize Achromosome. For example, any of the Z. mays chromosomes listed in Table1 may be used as a starting chromosome for making a minichromosome ofthe invention.

Table 1 illustrates the sizes for Zea mays A chromosomes in Megabasepairs (Mb) or in centimorgans (cM). The size in cM has determined viatwo different strategies as described in Sharpopova et al., 2002.

TABLE 1 Zea mays A chromosome sizes. Size Chromosome Mega base pairs(Mb) IBM v2 (cM) UMC98 (cM) 1 337 975 248 2 278 612 207 3 259 685 166 4271 684 175 5 250 607 174 6 208 492 168 7 199 566 147 8 202 567 183 9191 581 150 10 170 472 134

It will also be understood that in some cases the minichromosomecomprises a site specific recombination site. Thus, any plant varietycomprising the minichromosome may be transformed with a vector thatenables the introduction of transgene into the minichromosome by sitespecific recombination. Once a plant minichromosome is generated it maybe easily introgressed into a desired genetic background by plantbreeding techniques that are well know in the art.

Thus, the present invention provides processes for breeding of plantsthat comprise a minichromosome. In accordance with such a process, afirst parent plant may be crossed with a second parent plant wherein thefirst and second plants comprise a minichromosome, or wherein at leastone of the plants comprises a minichromosome. For example, corn plants(Zea mays L.) comprising a minichromosome can be crossed by eithernatural or mechanical techniques.

Natural pollination occurs in flowering plants when wind or insectsspread pollen from a plant. However, mechanical pollination can beeffected by controlling the types of pollen that are introduced or bypollinating by hand. In one embodiment, crossing comprises the steps of:

-   -   (a) planting in pollinating proximity seeds of a first and a        second parent plant, and preferably, seeds of a first inbred        plant and a second, distinct inbred plant;    -   (b) cultivating or growing the seeds of the first and second        parent plants into plants that bear flowers;    -   (c) emasculating flowers of either the first or second parent        plant, i.e., treating the flowers so as to prevent pollen        production, or alternatively, using as the female parent a male        sterile plant, thereby providing an emasculated parent plant;    -   (d) allowing natural cross-pollination to occur between the        first and second parent plants;    -   (e) harvesting seeds produced on the emasculated parent plant;        and, where desired,    -   (f) growing the harvested seed into a plant, preferably, a        hybrid plant.

Parental plants are typically planted in pollinating proximity to eachother by planting the parental plants in alternating rows, in blocks orin any other convenient planting pattern. Where the parental plantsdiffer in timing of sexual maturity, it may be desired to plant theslower maturing plant first, thereby ensuring the availability of pollenfrom the male parent during the time at which the female parent isreceptive to pollen. Plants of both parental parents are cultivated andallowed to grow until the time of flowering. Advantageously, during thisgrowth stage, plants are in general treated with fertilizer and/or otheragricultural chemicals as considered appropriate by the grower.

At the time of flowering, in the event a plant comprising aminichromosome is the male parent, the pollen producing organs of theother parental plant are removed from all plants employed as the femaleparental plant to avoid self-pollination. This can be achieved manuallybut also can be done by machine, if desired. Alternatively, when thefemale parent plant comprises a cytoplasmic or nuclear gene conferringmale sterility, removal of the pollen producing organs may not berequired. Additionally, a chemical gametocide may be used to sterilizethe male flowers of the female plant. In this case, the parent plantsused as the male may either not be treated with the chemical agent ormay comprise a genetic factor which causes resistance to theemasculating effects of the chemical agent. Gametocides affect processesor cells involved in the development, maturation or release of pollen.Plants treated with such gametocides are rendered male sterile, buttypically remain female fertile. The use of chemical gametocides isdescribed, for example, in U.S. Pat. No. 4,936,904, the disclosure ofwhich is specifically incorporated herein by reference in its entirety.Furthermore, the use of ROUNDUP herbicide (Monsanto, St. Louis, Mo.) incombination with glyphosate tolerant corn plants to produce male sterilecorn plants is disclosed in PCT Publication WO 98/44140.

Following emasculation, the plants are then typically allowed tocontinue to grow and natural cross-pollination occurs as a result of theaction of wind, which is normal in the pollination of grasses, such ascorn. As a result of the emasculation of the female parent plant, allthe pollen from the male parent plant is available for pollinationbecause pollen bearing flowering parts, have been previously removedfrom all plants of the plant being used as the female in thehybridization. Of course, during this hybridization procedure, theparental varieties are grown such that they are isolated from otherplant fields to minimize or prevent any accidental contamination ofpollen from foreign sources. These isolation techniques are well withinthe skill of those skilled in this art.

Both parental plants of a cross may be allowed to continue to grow untilmaturity or the male rows may be destroyed after flowering is complete.Only the seeds from the female parental plants are harvested to obtainthe seeds of a novel F₁ hybrid. The novel F₁ hybrid seed produced canthen be planted in a subsequent growing season in commercial fields or,alternatively, advanced in breeding protocols for purposes of developingnovel inbred lines.

Alternatively, in another embodiment of the invention, one or both firstand second parent plants can comprise a plant minichromosome. Thus, anyplant comprising a minichromosome of the invention forms a part of theinvention. As used herein, crossing can mean selfing, backcrossing,crossing to another or the same variety, crossing to populations, andthe like. All corn plants produced using plant comprising aminichromosome as a parent are, therefore, within the scope of thisinvention.

EXAMPLES

The following examples are included to further illustrate variousaspects of the invention. It should be appreciated by those of skill inthe art that the techniques disclosed in the examples that followrepresent techniques and/or compositions discovered by the inventor tofunction well in the practice of the invention, and thus can beconsidered to constitute preferred modes for its practice. However,those of skill in the art should, in light of the present disclosure,appreciate that many changes can be made in the specific embodimentswhich are disclosed and still obtain a like or similar result withoutdeparting from the spirit and scope of the invention.

Example 1 General Telomere Truncation Methods

Telomere-mediated chromosomal truncation is accomplished by theintroduction of six copies of telomere repeats into an endogenous plantchromosome via a transformation plasmid. In this particular case thetelomere repeats were made from Arabidopsis telomeres previously clonedby Richards and Ausubel (1988). Maize HiII (Armstrong and Green, 1985)immature embryos were transformed following the protocols forAgrobacterium-mediated transformation with a standard binary vector(Frame et al., 2002). During the Agrobacterium-mediated transformation,the T-DNA is protected by Agrobacterium VirD2 and VirE proteins, andintegrated into the plant genome by an illegitimate recombinationmechanism. Small deletions may occur mostly in the left border region,and sometimes in the right border region. However, these deletions willnot destroy the telomere sequence. The presence of the telomere repeatstruncates the chromosome upon integration. The telomere-associatedchromosome truncation has been demonstrated to occur, and has been usedto produce minichromosomes in mammalian cells (Farr et al., 1991, 1992,1995; Barnett et al., 1993; Itzhaki et al., 1992; Heller et al., 1996;Mills et al., 1999; Saffery et al., 2001). Using two telomere-mediatedchromosomal truncation constructs, it was demonstrated that six copiesof direct Arabidopsis telomere units could render chromosomal truncationin maize.

Two binary constructs for chromosomal truncation were constructed forAgrobacterium-mediated gene transformation of maize HiII immatureembryos (pWY76 and pWY86; see FIG. 1). Ninety three and eighty threetransgenic lines were recovered for pWY76 and pWY86, respectively. Afluorescence in situ hybridization (FISH) method (Kato et al., 2004) wasused to detect transgenes on metaphase chromosomes of T0 transgenicplants. A total of 123 transgene integration sites for pWY76 and 107sites for pWY86 were visualized, with 54 and 55 integration siteslocalized at the ends of chromosomes. Pollen abortion was also observedin transgenic lines in which chromosomal truncation occurred.Furthermore, deletions of distal FISH markers in several transgeniclines were detected by a karyotyping probe cocktail. For example, in onepWY76 transgenic line, the chromosome 3 short arm was truncated.Southern blot analysis demonstrated smear patterns of hybridization,which is a typical feature of heterogeneous newly seeded telomeres (Farret al., 1991). These studies indicated that chromosome truncationsoccurred in these transgenic lines. In contrast to the pWY76 and pWY86transgenes, two other constructs without the telomere repeats were alsotransformed simultaneously; however, no chromosomal truncationsobserved. These results indicated that the telomere repeats were thecause of chromosome truncation.

An A chromosome derived mini-chromosome was found in one pWY86 line byFISH screening. This mini-chromosome was found to originate fromchromosome 7 with most of the long arm deleted. This mini-chromosome wasoriginally found in a tetraploid line without B chromosomes. Because itoccurred in a polyploid, the deficiency caused by the truncation of thechromosome was compensated by its homologues in diploid gametophytes. Infact, the typical 50% pollen abortion observed in diploid lines with onechromosome deficiency was not observed, and progenies containing thismini-chromosome were recovered after crossing the recovered transformantby a diploid plant, which reduced the ploidy level to triploid. Theploidy level was further reduced to diploid plus the minichromosome inboth HiII and Mo17 backgrounds. Further studies showed that thisminichromosome did not cause any abnormal phenotypes. The minichromosometransmitted at 38.5% (10/26) rate as male when crossed to a diploidplant.

Nucleic Acid Constructs for Telomere Truncation in Plants

Two truncating constructs and a telomere-minus control were constructedby using the binary vector pTF101.1 (Paz et al., 2004) and used for theminichromosome production (see FIG. 1 for maps of constructs).Components on these constructs are listed in order as below: pWY76:LB-Tvsp-Bar-2XP35S-lox66-GFP-Tnos-Pmas-HPT-Tmas-6x telomeres-RB, pWY86:LB-Tvsp-Bar-2XP35S-lox71-DsRed-Tnos-Pnos-FRT-FLP-Tnos-6x telomeres-RBand pWY96: LB-Tvsp-Bar-2XP35S-lox71-DsRed-Tnos-Pnos-FRT-FLP-Tnos-Pmas-HPT-Tmas-RB

Promoterless lox66-GFP, or lox71-DsRed fusion genes were included inpWY76 and pWY86, respectively, to allow further gene specificintegration at the lox site. In addition, a Pnos-FRT-FLP-Tnos cassettewas included in pWY86 to allow site-specific recombination at the FRTsite for further gene integration.

Example 2 Telomere Truncation in B-Chromosomes

To produce mini-B chromosomes by telomere-mediated chromosomaltruncation, B chromosomes from Black Mexican Sweet (BMS) corn cells wereintroduced into a maize HiII parent A line and allowed to accumulate tomulti-copies. The two telomere-associated chromosomal truncationconstructs were mixed with a pACH25 construct (Christensen and Quail,1996) for targeting HiII hybrid or HiII parent A immature embryos withmultiple B chromosomes by biolistic transformation (Frame et al., 2000).The bar gene driven by a maize ubiquitin promoter in the pACH25construct enables efficient selection of transgenic events on mediasupplemented with bialaphos. Telomere sequences on the constructstruncate B chromosomes as well as A chromosomes once integrated into thechromosomes, thus both minichromosomes from truncated B and Achromosomes can be produced. Root tip metaphase chromosomes obtainedfrom regenerated herbicide resistant plants (T0) were screened by FISHfor minichromosomes. The pACH25 plasmid and a pWY96 construct (seeExample 1), which has almost all other sequences of both pWY76 and pWY86(see below) except the telomere sequence, are used as probes for FISHscreening. The pWY96 probe can efficiently hybridize with both the pWY76and pWY86 transgenes. A B-repeat probe was used to identify truncationsof the B chromosomes (Alfenito and Birchler, 1993). Forty eightminichromosomes were identified; 41 of which were from the B chromosomewhile 7 were from an A chromosome. All minichromosomes from Bchromosomes were transmissible and most of them were recovered in the T1generation. A chromosome doubling treatment (Kato and Birchler, 2006)was conducted on three truncated A minichromosomes to preserve theminichromosomes as they would otherwise be lost in meiosis if maintainedin a diploid.

Example 3 Expression of Cre Gene by Agrobacterium-Mediated GeneTransformation with a BIBAC Vector System

A BIBAC™ vector system was adopted for maize transformation with a largepiece of genetic material including a herbicide resistance marker gene,a 30 kb yeast genomic DNA as a marker for fluorescence in situhybridization (FISH), and a 35S-lox-Cre recombination cassette. Briefly,the BIBAC gene transformation plasmid pJV21 was constructed as follows.The pCH20 vector (Hamilton, 1997) was modified to deleted the BamHI toSwaI fragment. The BamHI site was reconstituted by adding a BamHI linkerat the SwaI site followed with BamHI digestion and re-ligation. Theresulting plasmid is named pJV06. A 3.4 kb HindIII/SalI fragmentcontaining the 35S-loxP-Cre gene expression cassette from pED97 wascloned into the BamHI site by blunt end ligation to make pJV08. Next, a400 bp telomere sequence and a ubi-bar gene expression cassette frompAHC25 (Christensen et al., 1992) were assembled in pBLUESCRIPT™(Strategene, La Jolla, Calif.) and then cloned into the SrfI site ofpJV08 by blunt end ligation to make pJV15 in which the telomere sequencewas placed at the left border of the binary vector. The ubi-bar gene wasused as a selection marker for these studies. The telomere sequenceTTTAGGG (SEQ ID NO:1) was orientated towards the left border. Another400 bp telomere sequence was cloned into the PacI site by blunt endligation to make a direct repeat of the 800 bp of telomere sequence atthe LB. The clone was sequenced to confirm the orientation of thetelomere repeat. A 30 kb yeast DNA from BIBAC1 (Hamilton, 1997; Hamiltonet al., 1996) was then cloned into the NotI site to make pJV21 (FIG. 2).Constructs were transferred to Agrobacterium strain LBA4404 byelectroporation of competent cells following the manufacturer'sinstructions (Gibco, Invitrogen Co., Carlsbad, Calif.). In thisconstruct, a 35S-lox66-Cre cassette was cloned adjacent to the rightborder in order to place the Cre/lox site-specific recombination systeminto the genome by gene transformation.

Genetic Transformation

An Agrobacterium-mediated gene transformation was performed with thepJV21 construct to transform immature embryos of HiII plants with 0 to12 B chromosomes. Seventy-five transformed lines were recovered. Thetransgenes were confirmed by Southern hybridization and FISH (Kato etal., 2004). In 60 lines characterized by Southern hybridization, 45lines had a single copy transgene. Sixty-three of the 75 transgeniclines had a single transgene as determined by FISH. The transgeneintegrity was analyzed by Southern blot hybridizations at both the leftand the right ends of the T-DNA region using probes of the bar gene andthe Cre gene, respectively. In the 75 lines that were analyzed, 52transgenic lines were found to have the same copy number at both theleft and the right border, indicating that the transgenes in these casesare intact.

Integration of a Transgene into the Telomere Region

One transgenic event J11-9 showed a smear pattern of Southernhybridization as compared to the others that have discrete bands. Thesmear pattern of hybridization is a hallmark of telomeres that resultfrom natural telomere activity or neo-telomeres seeded during atelomere-mediated chromosomal truncation, because the telomerase addsdifferent numbers of the telomeric motif TTTAGGG; (SEQ ID NO:1) indifferent cells (Farr et al., 1991; Richards and Ausubel, 1988). Todemonstrate the terminal nature of this transgene, multiple restrictionenzymes that cut the distal region of the transgene just preceding the800 bp telomere repeat were used to digest the J11-9 genomic DNA, and aSouthern hybridization was performed with a ³²P-labeled bar gene probeas described (Yu et al., 2006b). The smear patterns of hybridizationshifted according to the distances between the three restriction enzymecutting sites (XbaI, XhoI and DraI) and the telomeric ends of thechromosome. For example, the most proximal enzyme DraI generated thelargest sized smear pattern in the range of more than 6 kb, while themost distal one XbaI generated a smear patterns in the range of 3.2 to4.6 kb and the XhoI produced smears between 5 to 6 kb. In contrast, thecleavage at a more proximal HindIII site produced a discrete band. Adiscrete band would be generated if there is a HindIII site distal tothe bar gene probe. This HindIII site was likely present at the naturaltelomere because this site was not found in our sequence data of thepJV21 construct. Thus, the end position of the transgene in J11-9 waspotentially the result of an integration event within the telomeresrather than a de novo telomere formation. In addition, no abnormalgrowth, gametophyte sterility, or reduced transmission has been observedin the J11-9 plants, indicating that there is no functional geneticmaterial loss caused by this transgene, a phenomenon frequently observedin transgenic plants with chromosomal truncations (Yu et al., 2006b).

The end location of this transgene was also revealed by a cytologicalanalysis. Chromosomes from J11-9 root tips were hybridized with aFluorescein-dUTP labeled 30 kb DNA probe mixed with a karyotypingcocktail (Kato et al., 2004). The karyotypes of Hill transformationrecipients were produced with this cocktail (Yu et al., 2006a). Thetransgene was identified at the end of chromosome arm 3L.

Position and the Distribution of Transgenes

The FISH analysis was extended to all the transgenic lines in order toprofile the transgene positions and distributions. Transgenes were foundin every chromosome of the karyotype (Table 2) and integration siteswere found in or near telomeres, centromeres, euchromatic regions,heterochromatic knobs and NOR regions by FISH. All chromosome arms wereincluded except 8S and 10S. The transgenes were distributed randomlyamong the 10 A chromosomes with greater numbers on large chromosomes,and less numbers on small chromosomes as expected. However, no transgenewas observed on any B chromosome although there were up to 12 Bchromosomes (“Bs”) present (average 3.9) in the transformed plants.

TABLE 2 Transgenic events with the pJV21 construct of maize byAgrobacterium-mediated transformation. Trans. Southern FISH CreChromosome Line Bs bar Cre Y30 Activity location 10-1 4 1 1 1 + 1L,Satellite 10-2 5 1 1 1 + 1S 10-3 1 1 1 1 + 1S, Distal 10-4 3 1 1 1 + 1S10-5 3 1 2 1 + 5S, Distal 10-6 4 1 0 1 + 6L 10-7 2 1 0 1 − 10L, VeryDistal 11-1 4 1 1 1 + 7L, Cent.-Knob-Y30 11-2 0 1 1 2 + 2L + 7L, 2L =Sat.-Y30-5SRNA, 7L = Distal 11-3 6 3 3 3 + 2C + 4S + 5L, 2C =Centromeric, 4S = Satellite, 5L = Middle 11-5 3 1 1 1 + 5L,Sat.-Y30-Knob 11-6 4 1 2 1 + 2S, Cent.-Y30-Sat. 11-7 6 1 1 1 + 1L 11-8 32 3 1 + 1S, Cent.-Y30-Knob 11-9 5 1 1 2 + 3L + 5L, 3L = Very Distal, 5L= Distal 11-10 8 1 0 1 − 10L, Distal 11-11 3 2 1 1 + 7L, Knob 11-12 1 11 1 + 1L, Distal 11-13 2 1 1 1 + 7L, Distal 11-14 4 1 1 1 + 1L 11-15 3 31 1 + 1S, Middle 11-16 4 3 1 1 + 6L, Middle 11-17 6 2 2 2 + 7L + 7S, 7L= Cent.-Y30-Knob 11-18 6 1 2 1 + 3S, Distal 11-19 2 1 1 1 + 7L 11-20 5 11 1 + 9S, Cent.-Y30-Knob 11-21 5 3 0 1 − 2C, Centromeric 11-22 3 2 0 1 −11-23 8 1 2 1 + 1L, Satellite 11-24 7 1 1 1 + 7L 11-25 7 1 1 1 + 3L,Distal 11-26 2 2 2 2 + 2L + 9L, 2L = Middle, 9L = Distal 11-27 6 1 1 1 +10L, Distal 11-28 4 1 1 1 + 5L, Distal 11-29 9 1 2 1 + 3S, Distal 11-301 1 1 1 + 5L, Knob 11-31 4 1 1 2 + 7L + 10L, 7L = Knob, 10L = VeryDistal 11-32 2 1 1 1 + 4L, Distal 12-1 6 1 1 2 + 2L + 7S 12-2 3 3 3 1 −3S 12-3 11 2 2 2 + 4L, Middle 12-4 6 1 1 1 + 9L, Distal 12-5 5 1 2 1 +7L, Distal 12-6 0 1 1 1 + 8L, Very Distal 12-7 2 1 1 1 + 5L 12-8 0 1 21 + 1L + 3L + 6S, 1L = Distal to Sat. 12-9 2 1 1 1 + 4S, Proximal toSat. 12-10 1 1 1 1 + 2S, Distal 12-11 5 1 1 1 + 9L, Middle 12-12 0 1 11 + 5L, Distal 12-13 2 1 1 1 + 4S, Cent.-Y30-Sat. 12-14 2 1 1 1 + 8L,Knob 12-15 2 1 0 1 + 4L, Middle 12-16 11 1 1 1 + 3L, Middle 12-17 6 1 11 + 4L, Middle 12-18 6 1 1 1 + 5L, Middle 12-19 4 3 3 1 + 6L, Distal12-20 6 4 2 2 + 1L + 10L, 1L = In the Sat., 10L = Distal 12-21 0 2 1 1 +2L, Middle 12-22 3 2 1 1 + 3L, Middle 12-23 1 1 0 0 − 12-24 7 1 1 1 +8L, Knob 12-25 4 1 2 1 + 2L, Cent.-Sat.-Y30 12-26 5 1 1 1 + 10L, Distal12-27 9 1 1 1 + 1S, Middle 12-28 3 1 1 1 + 12-29 2 1 1 1 + 3L, Middle12-30 5 1 0 1 + 1L 12-31 4 1 1 1 + 6S, NOR 12-32 4 1 1 1 + 3S, Distal12-33 2 1 1 1 + 3L, Middle 12-34 3 1 1 1 + 2S, Distal 12-35 4 1 1 1 −8L, Cent.-Y30-Knob 12-36 0 1 1 1 + 8L 12-37 2 1 1 2 + 1S + 6L, 1S =Knob, 6L = Distal

Cre/Lox Site-specific Recombination System

The transformation with the BIBAC construct placed 84 transgenesrandomly into the maize genome. These transgenes are mostly intact asindicated by Southern hybridizations. Ninety-one transgenic sites weredetected in 75 transgenic lines by Southern hybridizations with a Cregene probe (Table 2). To demonstrate that these Cre transgenes wereexpressed and functional, a reporter construct pHK52 (Srivastava et al.,1999) was biolistically delivered into the immature embryos of theprogeny of the transgenic plants. The pHK52 construct contains anantisense orientated beta-glucuronidase (GUS) gene under the maizeubiquitin promoter. The antisense GUS gene is flanked by invertedrepeats of the loxP site. The antisense GUS gene can be reverted to thesense orientation and expressed at the presence of a Cre recombinasewhich catalyzes the inversion of genetic elements flanked by invertedrepeats of lox sites. A transient GUS assay was performed on bombardedembryos from all transgenic lines. This study demonstrated the Cre genewas functional in 68 lines (Table 2). An embryo population wassegregating for the transgene in an outcross of J11-9 to the HiII line.GUS expression was activated in 30 out of a total of 50 embryos, a ˜1:1ratio.

Example 4 Telomere Truncation of B Chromosomes by Particle BombardmentTransformation

Since the B-chromosome has many properties that make it preferable foras a minichromosome, further studies were performed to determine whetherplant minichromosomes derived from B chromosomes may be efficientlygenerated. Telomere truncation constructs, pWY76 and pWY86 (FIG. 1) wereused in these studies. Additionally, plasmid pWY86-bar was made bydigesting pWY86 with PmlI/AvrII and self-ligation to delete the 35S-bargene expression cassette. Plasmid pAHC25 used in the studies has beenpreviously described by Christensen and Quail (1996).

Briefly, immature embryos between 1.2 to 2.0 mm were dissectedaseptically in a flow hood. Biolistic-mediated gene transformation ofmaize immature embryos was conducted as described by Songstad et al.(1996) and Frame et al. (2000). Immature embryos were placed face downon callus initiation media with N6 salts and vitamins (Chu et al., 1975)supplemented with 2.0 mg/l 2,4-D, 100.0 mg/l myo-inositol, 2.8 μlproline, 30.0 μl sucrose, 100.0 mg/l casein hydrolysate, 3.0 μl GELRITE,25 μM silver nitrate, PH 5.8. Embryos were induced at 28° C. for 2-4days, then transferred to osmotic media with N6 salts and vitaminssupplemented with 2.0 mg/l 2, 4-D, 100.0 mg/l myo-inositol, 0.7 μlproline, 30.0 μl sucrose, 100.0 mg/l casein hydrolysate, 36.4 μlsorbitol, 36.4 μl mannitol, 3.0 μl GELRITE, 25 μM silver nitrate, pH 5.8for 4 hours osmotic treatment prior to bombardment.

Plasmids were prepared with a Qiagen miniprep kit (Qiagen, Valencia,Calif.). Three milligrams of 0.6μ gold particles (BIO-RAD, Hercules,Calif.) were coated with the mixture of 1 μg telomere truncation plasmid(pWY76, pWY86, or pWY86-bar) and 0.25 μg pAHC25. The bombardment wascarried out with the PDS 1000/He biolistic gun (BIO-RAD) using thefollowing parameters: 650 psi rupture disk pressure, 6 cm targetdistance, 6 mm gap, 1.2 cm from macro-carrier to stopping plate, and 28Torr vacuum at rupture.

Bombarded embryos on the osmotic media were wrapped with PARAFILM andincubated at 28° C. overnight and then transferred to callus initiationmedia the next morning.

FISH Analysis of Mini-chromosomes in Transgenic Plants

T0 transgenic plants were screened for mini-chromosomes by FISH asdescribed above. Probes of pWY96 and pAHC25 were labeled with Texas reddCTP by nick translation (Kato et al., 2004) and hybridized totransgenes. B repeat sequence (Alfenito and Birchler 1993) was labeledwith Alexa Fluor-488 dCTP, and mixed with either pWY96 or pAHC25transgene probes to screen transformed B chromosomes bybiolistic-mediated transformation. CentC (Ananiev et al., 1998) and NOR(Stein et al., 1998) probes were labeled with Alexa Fluor-488 dCTP(Invitrogen); CRM (Zhong et al., 2000) was labeled with Cy5-dCTP.Minichromosomes were identified by their size as compared to normal A orB type chromosomes. FISH of meiotic cells was performed as described byGao et al. (1999) and Yu et al. (2006). B repeat was labeled with Texasred dCTP and the knob sequence (14) was labeled green with AlexaFluor-488 dCTP.

Two hundred eighty one transgenic events were regenerated from bialaphosresistance calli (67 with pWY76, 87 with pWY86, and 127 with pWY86-bar).FISH revealed that forty one events had transgenes on B chromosomes,which included 24 mini-chromosomes with distal transgenes and 20 intactB chromosomes with internal transgenes. Additionally, 5 A-B and 1 B-Atranslocations, and 7 fragments from A chromosomes were identified.Finally, 10 truncated B chromosome derivatives without transgene signalswere also identified. These events were likely produced whentelomere-mediated chromosomal truncation occurred in such an orientationthat the transgenes are retained on acentric fragments and are lostduring mitosis. These mini-chromosomes would be lost during selection inthe transformation process if they had not been supported by additionaltransgenes in the same event. Thus, these minichromosomes were fewer innumber than those with transgenes.

Minichromosome Size Measurement

To measure the size of the B centromere repeat of 86B23, the greenchannels of 10 metaphase chromosome images that has B repeat labeledgreen were imported to the Fujifilm Image Gauge V3.3 program (Fuji,Tokyo, Japan). The quantity of the minichromosome centromere and that ofa normal B chromosome centromere were measured and the ratio of themini-chromosome centromere to that from a normal B was calculated fromeach individual cell. The average ratio and standard deviation werecalculated. To measure the chromosome size of 86B23, the pachytenechromosomes were stained with 4′-6-Diamidino-2-phenylindole (DAPI),images were captured via a Zeiss fluorescence microscope (Carl Zeiss,Inc., Oberkochen, Germany) and imported to Fujifilm Image Gauge program(Fuji). The lengths of the mini-chromosome and the normal B chromosomewere measured, and their ratio was calculated. The sizes of othermini-chromosomes were estimated visually based on their appearance ascompared with those of normal B chromosomes in the same cell. Sizecomparisons of several truncated B chromosomes are shown in Table 3.

Transmission Test of Mini-chromosomes

Results from these studies showed that transmission of mini-chromosomesduring meiosis varies (Table 3). The transmission of a univalent R2(34.8% from a self-pollination) was comparable with a previouslyreported isochromosome 8S•8S (37.5%) (Yu et al., 2006). The transmissionof B type mini-chromosomes varies from 12% (86-74) to 39% (76-15a) viathe male parent (Table 3). Transmission of mini-chromosomes was affectedby many factors, such as a chromosome size limit (Schubert, 2001; Spenceet al., 2006). It is also known that the B centromere size and structurecan affect the transmission of B chromosome derivatives (Kaszas andBirchler 1998). Most of the B chromosome derived minichromosomesunderwent nondisjunction in the presence of normal B chromosomes. The Bchromosome long arm distal region and the centromere are responsible fornondisjunction of B chromosomes (Carlson 1978). For example, in thepresence of normal B chromosomes, male parents transmitted 2 copies ofmini-chromosomes to the progeny (Table 3). This property of B typemini-chromosomes provides a mechanism to create a dosage series of themini-chromosomes for increased expression of genes of interest.

TABLE 3 B minichromosome sizes and transmission rates. Events 76-15a86-74 86B23 86B155 R2 Chromosome Size ½ B ⅕ B 1/20 B ¾ B NM TransgeneLocation distal distal distal distal distal Cross as male as male asmale self self Transmission 14/36 3/25 7/29  9/18 15/46 Transmission*30/36 6/25 8/29 16/18 16/46 NM indicates not measured. *Number ofprogeny with minichromosomes/number of progeny tested. **Number ofminichromosomes transmitted/number of progeny tested.

Histochemical GUS Assay in Individuals of Transgenes on B Chromosomesand Derivatives

As with supernumerary B chromosomes from other organisms, the Bchromosome of maize is inert without any detected active genes (Jones,1995). However, it is not known whether the lack of gene activity on Bchromosomes is caused by the absence of genes or because of suppressionof gene transcription by the B chromosome due to its heterochromaticnature. The transformation of the B chromosome in maize is used todetermine whether there is suppression of transgene expression. In thisstudy 17 transgenic events were recorded that had only transgenes on Bchromosomes. This indicated that they were probably supported by thetransgenic bar gene expression from B chromosomes, although it waspossible that transgenes on A chromosomes were present but were toosmall to be detected by the FISH method. GUS gene expression from 9 ofthese events were determined by assaying the resistant calli. Theabsence of GUS expression from other events can be attributed to eitherthe silencing of the GUS gene or the absence of an intact GUS genecassette during the transformation process. However, in at least 6events, the GUS gene expression was attributed to the transgenes on Bchromosome or derivatives (Table 4). In these cases, primary rootsgerminated from segregating progeny were tested for GUS expression. Forexample, in the progeny of 76-15a, 76-15b and 86-74 outcrossed torecipient strain plants, all progeny that had transgenes on the Bchromosome or truncated derivatives (14, 11 and 3 individuals,respectively) expressed GUS, but none of them that did not havetransgenes on the B chromosomes or derivatives (22, 19 and 22individuals, respectively) expressed GUS. In progeny of self pollinated86B23 that had the smallest mini-chromosome, 23 out of 25 individualsthat had transgenes on the mini-chromosomes expressed GUS, but none ofthe 26 that did not have the mini-chromosome showed GUS expression. Theabsence of GUS expression from progeny lacking the transgenes on the Bchromosome and derivatives demonstrated that the GUS expression was fromthe transgenes on the B chromosome or derivatives and not undetectedA-chromosome events. Thus transgenes inserted into the B chromosomeswere expressed, at least in those sites that were tested. These sitesseem to be randomly distributed along the B chromosome from thecentromere to the end of the long arm of the B chromosome.

TABLE 4 Transgene expression in B minichromosomes. Events 76-15a 76-15b86-74 86B23 86B155 76-10 86-14 Chromosome Size ½ B 1B ⅕ B 1/20 B ¾ B 1 B1 B Transgene Location distal internal distal distal distal distalcentromere GUS+ 14 11 3 23 7 2 16 Total 14 11 3 25 9 12 23 % 100.0 100.0100.0 92.0 77.8 16.7 69.6

Histochemical assay of GUS gene expression was performed according toJefferson et al. (1987) by a GUS staining kit (Sigma, St. Louis, Mo.).Calli or cut roots of 2 to 5 mm long were placed directly into a 50 μlGUS staining solution arrayed in a 96 well PCR plate. The plate waswrapped with PARAFILM and incubated at 37° C. for 1 hour.

Recombination between J11-9 and R2

To demonstrate the use of mini-chromosomes as an AC platform, the loxsite on the R2 mini-chromosome was tested for Cre catalyzed exchange. Atransgenic plant J11-9 with a distal transgene 35S-lox66-Cre expressioncassette was crossed as a female by R2, which contains a promoterlesslox71-DsRed (Clontech, Mountain View, Calif.) gene. Lox66 and lox71 aremutated lox recombination sites that can recombine most favorably in theforward reaction, as described above. Successful recombination of thetwo transgenes results in the exchange of the distal regions of the twotransgenes and the addition of genetic material to the R2mini-chromosome from J11-9. The recombination can be monitored by thereciprocal reaction that places the promoterless DsRed gene under thecontrol of 35S promoter, thus producing a recognizable red fluorescenceprotein. The recombination events were screened on primary roots ofgerminated seedlings using a fluorescence stereo microscope with a Texasred filter. Four plants were identified based on the fluorescence assayfrom a total of 44 F1 progeny from a cross of heterozygous J11-9 byheterozygous R2. Approximately 8.7% of the progeny (about 4 plants)should have both of the transgenes based on the transmission of R2(Table 4) and J11-9.

To determine whether the red fluorescence was a result of site-specificrecombination, genomic DNA was isolated from each of the 4 plants thatexpressed red fluorescence, and was used as templates for PCRamplification across both of the predicted recombination products. Theamplified products were sequenced and recombination at the lox site wasconfirmed in each case. The configurations of the sequenced regionsmatched the expected patterns. Thus, this minichromosome wasdemonstrated to be amenable for genetic manipulations via asite-specific recombination system, and can serve as a prototype ofminichromosome based artificial chromosomes (ACs).

REFERENCES

The references listed below are incorporated herein by reference to theextent that they supplement, explain, provide a background for, or teachmethodology, techniques, and/or compositions employed herein.

-   U.S. Pat. No. 3,710,511-   U.S. Pat. No. 3,861,709-   U.S. Pat. No. 4,654,465-   U.S. Pat. No. 4,727,219-   U.S. Pat. No. 4,769,061-   U.S. Pat. No. 4,810,648-   U.S. Pat. No. 4,940,835-   U.S. Pat. No. 4,959,317-   U.S. Pat. No. 4,975,374-   U.S. Pat. No. 5,270,201-   U.S. Pat. No. 5,322,789-   U.S. Pat. No. 5,445,961-   U.S. Pat. No. 6,262,341-   U.S. Pat. No. 5,445,961-   U.S. Pat. No. 5,527,695-   U.S. Pat. No. 5,530,191-   U.S. Pat. No. 5,538,880-   U.S. Pat. No. 5,550,318-   U.S. Pat. No. 5,625,132-   U.S. Pat. No. 5,658,772-   U.S. Pat. No. 5,684,242-   U.S. Pat. No. 5,689,041-   U.S. Pat. No. 5,733,744-   U.S. Pat. No. 5,736,369.-   U.S. Pat. No. 5,741,684-   U.S. Pat. No. 5,929,301-   U.S. Pat. No. 6,175,058-   U.S. Pat. No. 6,187,994-   U.S. Pat. No. 7,015,372-   Abe et al., J. Biol. Chem., 262:16793, 1987.-   Abremski et al., Cell, 32(4):1301-1311, 1983.-   Albert et al., Plant J., 7(4):649-659, 1995.-   Albert et al., Plant J., 7:649-659, 1995.-   Alfenito and Birchler, Genetics, 135:589-597, 1993.-   Ananiev et al., Proc Natl Acad Sci USA, 95:13073, 1998.-   Araki et al., J. Mol. Biol., 225(1):25-37, 1992.-   Araki et al., Nucleic Acids Res., 25(4):868-872, 1997.-   Armstrong and Green, Planta, 164:207-214, 1985.-   Arondel et al., Science, 258(5086):1353-1355, 1992.-   Barnett et al., Nucleic Acids Res., 21:27-36, 1993.-   Beachy et al., Ann. Rev. Phytopathol., 28:451, 1990.-   Brock and Pryor, Chromosoma, 104:575-584, 1996.-   Chang, In Plant Breeding in the 1990s, Stalker and Murphy (Eds.),    Wallingford, U.K., CAB International, 17-35, 1992.-   Chase and Gabay-Laughnan, In Molecular Biology and Biotechnology of    Plant Organelles, Daniell and Chase, (Eds.), pp. 593-621, 2004.-   Christensen et al., Plant Molecular Biology, 18:675-689, 1992.-   Choi et al., Nucleic Acids Res., 28(7):E19, 2000.-   Christensen and Quail, Transgenic Res., 5:213-218, 1996.-   Chu et al., Sci. Sin., 18:659, 1975.-   Conger et al., Plant Cell Reports, 6:345-347, 1987.-   Cox, Proc. Natl. Acad. Sci. USA, 80(14):4223-4227 1983.-   Craig, Ann. Rev. Genetics, 22:77-105, 1988.-   Dale and Ow, Proc. Natl. Acad. Sci. USA, 88(23):10558-10562, 1991.-   Day et al., Genes Dev., 14(22):2869-2880, 2000.-   DeGreef et al., Bio/Technology, 7:61, 1989.-   Duncan et al., Planta, 165:322-332, 1985.-   Duvick, Adv. Genet, 13:1-56, 1965.-   Elliot et al., Plant Molec. Biol., 21:515, 1993.-   Enomoto, et al., J. Bacteriol., 6(2):663-668, 1983.-   European Appln. 0 160 390-   European Appln. 0 242 246-   European Appln. 0 333 033-   European Appln. 0 616644-   European Appln. 1 035 208-   Farr et al., Embo J., 14:5444-5454, 1995.-   Farr et al., Nat. Genet., 2:275-282, 1992.-   Farr et al., Proc. Natl. Acad. Sci. USA, 88:7006-7010, 1991.-   Fisher et al., Plant Physiol., 102(3):1045-1046, 1993.-   Fox et al. Proc. Natl. Acad. Sci. USA, 90(6):2486-2490, 1993.-   Frame et al., Dev. Biol.-Plant, 36:21-29, 2000.-   Frame et al., Plant Physiol., 129:13-22, 2002.-   Fukushige and Sauer, Proc. Natl. Acad. Sci. USA, 89(17):7905-7909    1992.-   Futcher, Yeast, 4(1):27-40, 1988.-   Gabay-Laughnan et al., Genetics, 166:959-970, 2004.-   Gao et al., Acta Botanica Sinica, 41, 1999.-   Geiser et al., Gene, 48:109, 1986.-   Gleen et al., Plant Molec. Biology, 18:1185-1187, 1992.-   Golic and Lindquist, Cell, 59(3):499-509, 1989.-   Golic, Genetics, 137(2):551-563, 1994.-   Gordon-Kamm et al., The Plant Cell, 2:603-618, 1990.-   Green and Rhodes, Maize for Biological Research, 367-372, 1982.-   Hamilton et al., Proc. Natl. Acad. Sci. USA, 93:9975-9979, 1996.-   Hamilton, Gene, 200:107-116 1997.-   Hammock et al., Nature, 344:458-461, 1990.-   Hayes et al., Biochem. J., 285(Pt 1):173-180, 1992.-   Heller et al., Proc. Natl. Acad. Sci. USA, 93:7125-7130, 1996.-   Hoess et al., Nucleic Acids Res., 14(5):2287-2300, 1986.-   Hoess et al., Proc. Natl. Acad. Sci. USA, 79:3398, 1982.-   Huang et al., J. Bacteriol., 179(19):6076-6083, 1997.-   Huang et al., Proc. Natl. Acad. Sci. USA, 88:5292-5296, 1991.-   Huub et al., Plant Molec. Biol., 21:985, 1993.-   Ito et al., Nuc. Acid Res. 10:1755. 1982.-   Itzhaki et al., Nat. Genet., 2:283-287, 1992.-   Jefferson et al., EMBO J., 6:3901, 1987.-   Jiang et al., Trends in Plant Sci., 8:570-575, 2003-   Jones and Rees, B Chromosomes, Academic Press, NY, 1982.-   Jones et al., Science, 266:7891, 1994.-   Jones, New Phytol., 131:411, 1995.-   Kaszas and Birchler, Genetics, 150:1683, 1998.-   Kato et al., Proc. Natl. Acad. Sci. USA, 101:13554-13559, 2004.-   Kato et al., Cytogenet Genome Res, 109:156-165, 2005.-   Kato and Birchler, J. Hered., 97:39-44, 2006.-   Kirihara et al., Gene, 71(2):359-370, 1988.-   Knutzon et al., Proc. Natl. Acad. Sci. USA, 89(7):2624-2628, 1992.-   Langer et al., Nucleic Acids Res., 30(14):3067-3077, 2002.-   Lee and Saito, Gene, 216(1):55-65, 1988.-   Lee et al., EMBO J., 7(5):1241-1248, 1988.-   Liu et al., Proc. Natl. Acad. Sci. USA, 96:6535-6540, 1999.-   Logemann et al., Bio/technology, 10:305, 1992.-   Maeser and Kahmann, Mol. Gen. Genet., 230(1-2):170-176, 1991.-   Mariani et al., Nature, 347:737-741, 1990.-   Mariani et al., Nature, 357:384-387, 1992.-   Marshall et al., Theor. App. Genet., 83:435, 1992.-   Martin et al., Science, 262:1432, 1993.-   McClintock, Genetics, 23:215-376, 1938.-   McDonough et al., J. Biol. Chem., 267(9):5931-5936, 1992.-   Medberry, et al., Nucleic Acids Res., 23(3):485-490, 1995.-   Meyer-Leon et al., Cold Spring Harb. Symp. Quant. Biol., 49:797-804,    1984.-   Miki et al., Theor. App. Genet., 80:449, 1990.-   Mills et al., Hum. Mol. Genet., 8:751-761, 1999.-   Mindrinos et al., Cell, 23; 78(6):1089-1099, 1994.-   Murray and Szostak, Nature, 305:189-193, 1983.-   Murray and Szostak, Mol Cell Biol, 6:3166-3172, 1986.-   Nasuda et al., Proc Natl Acad Sci USA, 102:9842-9847, 2005.-   O'Gorman et al., Science, 251(4999):1351-1355, 1991.-   Ogilvie et al., Science 214:270, 1981-   Onouchi et al., Nucleic Acids Res., 19(23):6373-6378, 1991.-   Onouchi et al., Mol. Gen. Genetics, 247:653-660, 1995.-   Ow, Curr. Op. Biotech., 7:181-186, 1996.-   Page et al., Genetics, 159:291-302, 2001.-   Paz et al., Euphytica, 136:167-179, 2004.-   PCT Appln. US93/06487-   PCT Appln. WO 01/11058-   PCT Appln. WO 01/40492-   PCT Appln. WO 91/13972-   PCT Appln. WO 98/44140-   PCT Appn. WO 95/06128-   Pen et al., BioTechnology, 10:292, 1992.-   Przibilla et al., Plant Cell, 3:169, 1991.-   Raboy et al., Maydica, 35:383, 1990.-   Rao et al., In: Somatic Embyogenesis in Glume Callus Cultures, Maize    Genetics Cooperation Newsletter #60, 1986.-   Reddy et al. Plant Mol. Biol., 22(2):293-300, 1993.-   Richards and Ausubel, Cell, 53(1):127-136, 1988.-   Rieder, Int. Rev. Cytol., 79:1-58, 1982.-   Sadowski, Prog. Nucleic Acid Res. Mol. Biol., 51:53-91, 1995.-   Saffery et al., Proc. Natl. Acad. Sci. USA, 98:5705-5710, 2001.-   Sauer and Henderson, Proc. Natl. Acad. Sci. USA, 85(14):5166-5170,    1988.-   Sauer, Biotechniques, 16(6):1086-1088, 1994.-   Sauer, Methods, 14(4):381-392, 1998.-   Sauer, Mol. Cell. Biol., 7(6):2087-2096, 1987.-   Schubert, Cytogenet Cell Genet, 93:175, 2001.-   Senecoff et al., J. Mol. Biol., 201(2):405-421, 1988.-   Sergaard et al., J. Biol. Chem., 268:22480, 1993.-   Sharopova et al., Plant Mol Biol 48:463-81, 2002.-   Shen et al., Hum Mol Genet, 6:1375-1382, 1997.-   Shen et al., Curr Biol, 10:31-34, 2000.-   Shinohara et al., Chromosome Res, 8:713-725, 2000.-   Shiroza et al., J. BacteoL., 170:810, 1988.-   Songstad et al., Plant Cell Reports, 7:262-265, 1988.-   Songstad et al., In Vitro Cell Dev. Biol-Plant, 32:179, 1996.-   Spence et al., Chromosoma, 115:60, 2006.-   Srivastava et al., Proc. Natl. Acad. Sci. USA, 96:11117-11121, 1999.-   Stein et al., The Plant Journal 13:281, 1998.-   Steinmetz et al., Mol. Gen. Genet., 20:220, 1985.-   Sumitani et al., Biosci. Biotech. Biochem., 57:1243, 1993.-   Tavladoraki et al., Nature, 366:469, 1993.

Taylor et al., Seventh Int'l Symposium on Molecular Plant-MicrobeInteractions (Edinburgh, Scotland) Abstract #497, 1994.

-   Trinh and Morrison, J. Immunol. Methods, 244(1-2):185-193, 2000.-   Tomizuka et al., Nat Genet, 16:133-143, 1997.-   Tomizuka et al., Proc Natl Acad Sci USA, 97: 722-727, 2000.-   Van Damme et al., Plant Molec. Biol., 24:25, 1994.-   Van Hartingsveldt et al., Gene, 127:87, 1993.-   Voet et al., Genome Res, 11:124-136, 2001.-   Wallace et al., Nuc. Acids Res., 28(6):1455-1464, 2000.-   Yu et al., Genome, 49:700, 2006.-   Zheng et al., Genetics, 153:1435-1444, 1999.-   Zhong et al., Plant Cell, 14:2825, 2002.

1. A plant minichromosome produced by truncating one or both arms of astarting plant chromosome, wherein the minichromosome comprises a nativeplant centromere, a heterologous nucleic acid comprising an engineeredtelomere sequence, and a site-specific recombination site, and is stablytransmitted during mitosis and meiosis in a plant comprising theminichromosome that is of the same species as the plant from which thestarting plant chromosome was obtained.
 2. The plant minichromosome ofclaim 1, wherein about 25% to about 99.9% of the starting plantchromosome has been truncated.
 3. The plant minichromosome of claim 1,wherein the engineered telomere sequences comprise about 2 to 100telomere repeats.
 4. The plant minichromosome of claim 1, wherein theengineered telomere sequences are from Arabidopsis.
 5. The plantminichromosome of claim 1, wherein both arms of the starting plantchromosome have been truncated.
 6. The plant minichromosome of claim 1,wherein the minichromosome is from about 1 Mb to about 100 Mb in size.7. The plant minichromosome of claim 1, wherein the starting plantchromosome is an A chromosome.
 8. The plant minichromosome of claim 1,wherein the starting plant chromosome is a B chromosome.
 9. The plantminichromosome of claim 1, wherein the starting plant chromosome is froma dicot.
 10. The plant minichromosome of claim 9, wherein the startingplant chromosome is from a monocot.
 11. The plant minichromosome ofclaim 1, further comprising a transgene.
 12. A plant cell comprising theplant minichromosome of claim
 1. 13. A plant comprising the plantminichromosome of claim
 1. 14. A seed comprising the plantminichromosome of claim
 1. 15. A method of producing a plantminichromosome, comprising the steps of: (a) transforming a startingplant chromosome with a heterologous nucleic acid comprising at leasttwo telomere repeat sequences, wherein said plant chromosome furthercomprises a heterologous site-specific recombination site; and (b)allowing truncation of the starting plant chromosome to occur to producea plant minichromosome.
 16. The method of claim 15, further comprisingtransforming the starting plant chromosome with said site-specificrecombination site.
 17. The method of claim 15, wherein the telomererepeat sequences are from Arabidopsis.
 18. The method of claim 15,wherein both arms of the starting plant chromosome are truncated. 19.The method of claim 15, wherein the starting plant chromosome is an Achromosome.
 20. The method of claim 15, wherein the starting plantchromosome is a B chromosome.
 21. The method of claim 15, furthercomprising transforming the starting plant chromosome with a selectedcoding sequence.
 22. The method of claim 15, wherein the selected codingsequence confers a trait selected from the group consisting of insectresistance, herbicide tolerance, altered carbohydrate metabolism,altered fatty acid metabolism, disease resistance, male fertilityrestoration and pest resistance.
 23. The method of claims 15, whereinthe starting plant chromosome is comprised in a plant cell.